From 6bcf7186666a48b6519a45263815e843e24adc6b Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Mon, 19 Sep 2016 01:47:30 +0200
Subject: [PATCH] Complex properties with serialization completed
---
example/Vector/4_complex_prop/Makefile | 10 +-
example/Vector/4_complex_prop/main.cpp | 122 ++++++++++++++++++++-----
openfpm_data | 2 +-
openfpm_pdata.doc | 2 +-
src/Vector/vector_dist_comm.hpp | 122 ++++++++++++++++---------
src/Vector/vector_dist_unit_test.hpp | 1 +
6 files changed, 186 insertions(+), 73 deletions(-)
diff --git a/example/Vector/4_complex_prop/Makefile b/example/Vector/4_complex_prop/Makefile
index 646357e95..93fc158bd 100644
--- a/example/Vector/4_complex_prop/Makefile
+++ b/example/Vector/4_complex_prop/Makefile
@@ -5,17 +5,21 @@ CC=mpic++
LDIR =
OBJ = main.o
+OBJ_SER = main_ser.o
%.o: %.cpp
$(CC) -O3 -c --std=c++11 -o $@ $< $(INCLUDE_PATH)
-vect: $(OBJ)
+vect_cp: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
-all: vect
+vect_ser: $(OBJ_SER)
+ $(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS)
+
+all: vect_cp vect_ser
run: all
- source $$HOME/openfpm_vars; mpirun -np 2 ./vect
+ source $$HOME/openfpm_vars && mpirun -np 2 ./vect_cp && mpirun -np 2 ./vect_ser
.PHONY: clean all run
diff --git a/example/Vector/4_complex_prop/main.cpp b/example/Vector/4_complex_prop/main.cpp
index 915f2868e..028b2b33f 100644
--- a/example/Vector/4_complex_prop/main.cpp
+++ b/example/Vector/4_complex_prop/main.cpp
@@ -1,12 +1,19 @@
+/*! \page Vector_4_cp Vector 4 complex properties and serialization
+ *
+ * \subpage Vector_4_complex_prop
+ * \subpage Vector_4_complex_prop_ser
+ *
+ */
+
/*!
*
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
*
* [TOC]
*
*
- * # Vector 4 complex property # {#vector_example_cp}
+ * # Vector 4 complex properties # {#vector_example_cp}
*
*
* This example show how we can use complex properties in a vector
@@ -19,7 +26,7 @@ int main(int argc, char* argv[])
{
/*!
*
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
*
* ## Initialization and vector creation ##
@@ -29,13 +36,36 @@ int main(int argc, char* argv[])
*
* \snippet Vector/4_complex_prop/main.cpp vect create
*
- * In This this particular case every particle carry a scalar,
+ * In this this particular case every particle carry a scalar,
* a vector in form of float[3], a Point, a list
- * in form of vector of float and a list of custom structures
+ * in form of vector of float and a list of custom structures, and a vector of vector.
+ * In general particles can have properties of arbitrary complexity.
+ *
+ * \warning For arbitrary complexity mean that we can use any openfpm data structure with and arbitrary nested complexity.
+ * For example a openfpm::vector<aggregate<grid_cpu<openfpm::vector<aggregate<double,double[3]>>>,openfpm::vector<float>> is valid
+ * \verbatim
+
+ particle
+ *
+ vector
+ / \
+ / \
+ grid vector<float>
+ /\
+ / \
+ double double[3]
+
+ * \endverbatim
+ *
+ * Our custom data-structure A is defined below. Note that this data-structure
+ * does not have pointers
*
* \snippet Vector/4_complex_prop/main.cpp struct A
*
*
+ * \warning custom data structure are allowed only if they does not have pointer.
+ * In case they have pointer we have to define how to serialize our data-structure
+ *
*/
// initialize the library
@@ -82,20 +112,24 @@ int main(int argc, char* argv[])
// A listA
constexpr int listA = 4;
+ // A list of list
+ constexpr int listlist = 5;
+
//! \cond [vect create] \endcond
vector_dist<2,float, aggregate<float,
float[3],
Point<3,double>,
openfpm::vector<float>,
- openfpm::vector<A>>>
+ openfpm::vector<A>,
+ openfpm::vector<openfpm::vector<float>>> >
vd(4096,domain,bc,g);
//! \cond [vect create] \endcond
/*!
*
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
*
* ## Assign values to properties ##
@@ -135,7 +169,7 @@ int main(int argc, char* argv[])
vd.getProp<point>(p).get(1) = 1.0;
vd.getProp<point>(p).get(2) = 1.0;
- size_t n_cp = (float)10 * rand()/RAND_MAX;
+ size_t n_cp = (float)10.0 * rand()/RAND_MAX;
vd.getProp<listA>(p).resize(n_cp);
@@ -146,10 +180,17 @@ int main(int argc, char* argv[])
vd.getProp<list>(p).add(i + 30);
vd.getProp<listA>(p).get(i) = A(i+10.0,i+20.0);
- vd.getProp<listA>(p).get(i) = A(i+30.0,i+40.0);
- vd.getProp<listA>(p).get(i) = A(i+50.0,i+60.0);
}
+ vd.getProp<listlist>(p).resize(2);
+ vd.getProp<listlist>(p).get(0).resize(2);
+ vd.getProp<listlist>(p).get(1).resize(2);
+
+ vd.getProp<listlist>(p).get(0).get(0) = 1.0;
+ vd.getProp<listlist>(p).get(0).get(1) = 2.0;
+ vd.getProp<listlist>(p).get(1).get(0) = 3.0;
+ vd.getProp<listlist>(p).get(1).get(1) = 4.0;
+
// next particle
++it;
}
@@ -158,19 +199,15 @@ int main(int argc, char* argv[])
/*!
*
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
*
* ## Mapping and ghost_get ##
*
- * Particles are redistributed across processors but only the scalar,vector and the point
- * are communicated (properties 0,1,2). A lot of time complex properties can be recomputed and
- * communicate them is not a good idea. The same concept also apply for ghost_get
- *
- * \note OpenFPM <= 0.5.0 cannot communicate complex properties like a vector or other structure
- * that are not POD object
- *
- * \note OpenFPM > 0.5.0 Does not have such limitation
+ * Particles are redistributed across processors all properties are communicated but instead of
+ * using map we use map_list that we can use to select properties.
+ * A lot of time complex properties can be recomputed and communicate them is not a good idea.
+ * The same concept also apply for ghost_get. In general we choose which properties to communicate
*
*
* \snippet Vector/4_complex_prop/main.cpp vect map ghost
@@ -181,16 +218,16 @@ int main(int argc, char* argv[])
// Particles are redistribued across the processors but only the scalar,vector, and point properties
// are transfert
- vd.map_list<scalar,vector,point>();
+ vd.map_list<scalar,vector,point,list,listA,listlist>();
// Synchronize the ghost
- vd.ghost_get<scalar,vector,point>();
+ vd.ghost_get<scalar,vector,point,listA,listlist>();
//! \cond [vect map ghost] \endcond
/*!
*
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
*
* ## Output and VTK visualization ##
@@ -209,7 +246,44 @@ int main(int argc, char* argv[])
//! \cond [vtk] \endcond
/*!
- * \page Vector_4_complex_prop Vector 4 complex property
+ *
+ * \page Vector_4_complex_prop Vector 4 complex properties
+ *
+ * ## Print 4 particles in the ghost area ##
+ *
+ * Here we print that the first 4 particles to show that the list of A and the list of list are filled
+ * and the ghosts contain the correct information
+ *
+ * \snippet Vector/4_complex_prop/main.cpp print ghost info
+ *
+ */
+
+ //! \cond [print ghost info] \endcond
+
+ size_t fg = vd.size_local();
+
+ Vcluster & v_cl = create_vcluster();
+ if (v_cl.getProcessUnitID() == 0)
+ {
+ for ( ; fg < vd.size_local()+4 ; fg++)
+ {
+ std::cout << "List of A" << std::endl;
+ for (size_t i = 0 ; i < vd.getProp<listA>(fg).size() ; i++)
+ std::cout << "Element: " << i << " p1=" << vd.getProp<listA>(fg).get(i).p1 << " p2=" << vd.getProp<listA>(fg).get(i).p2 << std::endl;
+
+ std::cout << "List of list" << std::endl;
+ for (size_t i = 0 ; i < vd.getProp<listlist>(fg).size() ; i++)
+ {
+ for (size_t j = 0 ; j < vd.getProp<listlist>(fg).get(i).size() ; j++)
+ std::cout << "Element: " << i << " " << j << " " << vd.getProp<listlist>(fg).get(i).get(j) << std::endl;
+ }
+ }
+ }
+
+ //! \cond [print ghost info] \endcond
+
+ /*!
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
* ## Finalize ## {#finalize}
*
@@ -226,7 +300,7 @@ int main(int argc, char* argv[])
//! \cond [finalize] \endcond
/*!
- * \page Vector_4_complex_prop Vector 4 complex property
+ * \page Vector_4_complex_prop Vector 4 complex properties
*
* # Full code # {#code}
*
diff --git a/openfpm_data b/openfpm_data
index dbfc39c70..f378ee11c 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit dbfc39c70904fa40ac52d71e784cd6f54283f578
+Subproject commit f378ee11c3aa2be8d0fde9fe5308d86d1d705aa7
diff --git a/openfpm_pdata.doc b/openfpm_pdata.doc
index b16dc1c02..94101cdb7 100644
--- a/openfpm_pdata.doc
+++ b/openfpm_pdata.doc
@@ -38,7 +38,7 @@ PROJECT_NAME = "OpenFPM_pdata"
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 0.5.0
+PROJECT_NUMBER = 0.5.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
diff --git a/src/Vector/vector_dist_comm.hpp b/src/Vector/vector_dist_comm.hpp
index 9f45b1c49..a22e80561 100644
--- a/src/Vector/vector_dist_comm.hpp
+++ b/src/Vector/vector_dist_comm.hpp
@@ -84,6 +84,67 @@ class vector_dist_comm
//! replicated ghost particles that are local
size_t lg_m;
+ //! process the particle with properties
+ struct proc_without_prp
+ {
+ template<typename T1, typename T2> inline static void proc(size_t lbl, size_t cnt, size_t id, T1 & v_prp, T2 & m_prp)
+ {
+ m_prp.get(lbl).set(cnt, v_prp.get(id));
+ }
+ };
+
+ template<typename prp_object, int ... prp>
+ struct proc_with_prp
+ {
+ template<typename T1, typename T2> inline static void proc(size_t lbl, size_t cnt, size_t id, T1 & v_prp, T2 & m_prp)
+ {
+ // source object type
+ typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
+ // destination object type
+ typedef encapc<1, prp_object, typename openfpm::vector<prp_object>::layout_type> encap_dst;
+
+ // Copy only the selected properties
+ object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(id), m_prp.get(lbl).get(cnt));
+ }
+ };
+
+ //! It process one particle
+ template<typename proc_class, typename T1, typename T2, typename T3, typename T4> inline void process_map_particle(size_t i, long int & end, long int & id_end, T1 & m_pos, T2 & m_prp, T3 & v_pos, T4 & v_prp, openfpm::vector<size_t> & cnt)
+ {
+ long int prc_id = m_opart.template get<2>(i);
+ size_t id = m_opart.template get<0>(i);
+
+ if (prc_id >= 0)
+ {
+ size_t lbl = p_map_req.get(prc_id);
+
+ m_pos.get(lbl).set(cnt.get(lbl), v_pos.get(id));
+ proc_class::proc(lbl,cnt.get(lbl),id,v_prp,m_prp);
+
+ cnt.get(lbl)++;
+
+ // swap the particle
+ long int id_valid = get_end_valid(end,id_end);
+
+ if (id_valid > 0 && (long int)id < id_valid)
+ {
+ v_pos.set(id,v_pos.get(id_valid));
+ v_prp.set(id,v_prp.get(id_valid));
+ }
+ }
+ else
+ {
+ // swap the particle
+ long int id_valid = get_end_valid(end,id_end);
+
+ if (id_valid > 0 && (long int)id < id_valid)
+ {
+ v_pos.set(id,v_pos.get(id_valid));
+ v_prp.set(id,v_prp.get(id_valid));
+ }
+ }
+ }
+
/*! \brief Return a valid particle starting from end and tracing back
*
* \param end actual opart particle pointer
@@ -492,21 +553,7 @@ class vector_dist_comm
// Run through all the particles and fill the sending buffer
for (size_t i = 0; i < m_opart.size(); i++)
{
- size_t lbl = p_map_req.get(m_opart.template get<2>(i));
- size_t id = m_opart.template get<0>(i);
-
- m_pos.get(lbl).set(cnt.get(lbl), v_pos.get(id));
- m_prp.get(lbl).set(cnt.get(lbl), v_prp.get(id));
- cnt.get(lbl)++;
-
- // swap the particle
- long int id_valid = get_end_valid(end,id_end);
-
- if (id_valid > 0 && (long int)id < id_valid)
- {
- v_pos.set(id,v_pos.get(id_valid));
- v_prp.set(id,v_prp.get(id_valid));
- }
+ process_map_particle<proc_without_prp>(i,end,id_end,m_pos,m_prp,v_pos,v_prp,cnt);
}
v_pos.resize(v_pos.size() - m_opart.size());
@@ -523,17 +570,18 @@ class vector_dist_comm
* \param pb send buffer
*
*/
- template<typename prp_object,int ... prp> void fill_send_map_buf_list(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & prc_r, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<openfpm::vector<Point<dim,St>>> & m_pos, openfpm::vector<openfpm::vector<prp_object>> & m_prp)
+ template<typename prp_object,int ... prp> void fill_send_map_buf_list(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<openfpm::vector<Point<dim,St>>> & m_pos, openfpm::vector<openfpm::vector<prp_object>> & m_prp)
{
- m_prp.resize(v_cl.getProcessingUnits());
- m_pos.resize(v_cl.getProcessingUnits());
- openfpm::vector<size_t> cnt(v_cl.getProcessingUnits());
+ m_prp.resize(prc_sz_r.size());
+ m_pos.resize(prc_sz_r.size());
+ openfpm::vector<size_t> cnt(prc_sz_r.size());
- for (size_t i = 0; i < prc_r.size(); i++)
+ for (size_t i = 0; i < prc_sz_r.size(); i++)
{
// set the size and allocate, using mem warant that pos and prp is contiguous
m_pos.get(i).resize(prc_sz_r.get(i));
m_prp.get(i).resize(prc_sz_r.get(i));
+ cnt.get(i) = 0;
}
// end vector point
@@ -545,31 +593,11 @@ class vector_dist_comm
// Run through all the particles and fill the sending buffer
for (size_t i = 0; i < m_opart.size(); i++)
{
- size_t lbl = m_opart.template get<2>(i);
- size_t id = m_opart.template get<0>(i);
-
- m_pos.get(lbl).set(cnt.get(lbl), v_pos.get(id));
-
- // source object type
- typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
- // destination object type
- typedef encapc<1, prp_object, typename openfpm::vector<prp_object>::layout_type> encap_dst;
-
- // Copy only the selected properties
- object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(id), m_prp.get(lbl).get(cnt.get(lbl)));
-
- cnt.get(lbl)++;
-
- // swap the particle
- long int id_valid = get_end_valid(end,id_end);
-
- if (id_valid > 0 && (long int)id < id_valid)
- {
- v_pos.set(id,v_pos.get(id_valid));
- v_prp.set(id,v_prp.get(id_valid));
- }
+ process_map_particle<proc_with_prp<prp_object,prp...>>(i,end,id_end,m_pos,m_prp,v_pos,v_prp,cnt);
}
+ v_pos.resize(v_pos.size() - m_opart.size());
+ v_prp.resize(v_prp.size() - m_opart.size());
}
/*! \brief Label particles for mappings
@@ -616,6 +644,12 @@ class vector_dist_comm
lbl_p.last().template get<0>() = key;
lbl_p.last().template get<2>() = p_id;
}
+ else
+ {
+ lbl_p.add();
+ lbl_p.last().template get<0>() = key;
+ lbl_p.last().template get<2>() = p_id;
+ }
}
// Add processors and add size
@@ -930,7 +964,7 @@ public:
//! properties vector
openfpm::vector<openfpm::vector<prp_object>> m_prp;
- fill_send_map_buf_list<prp_object,prp...>(v_pos,v_prp,prc_r, prc_sz_r, m_pos, m_prp);
+ fill_send_map_buf_list<prp_object,prp...>(v_pos,v_prp,prc_sz_r, m_pos, m_prp);
v_cl.SSendRecv(m_pos,v_pos,prc_r,prc_recv_map,recv_sz_map);
v_cl.SSendRecvP<openfpm::vector<prp_object>,decltype(v_prp),prp...>(m_prp,v_prp,prc_r,prc_recv_map,recv_sz_map);
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 413bf7aac..a4ef53344 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -1773,6 +1773,7 @@ BOOST_AUTO_TEST_CASE( vector_dist_ghost_put )
#include "vector_dist_cell_list_tests.hpp"
#include "vector_dist_NN_tests.hpp"
+#include "vector_dist_complex_prp_unit_test.hpp"
BOOST_AUTO_TEST_SUITE_END()
--
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